Docker image cutadapt does not use pigz
I tested zarp on a local machine and when the rules with cutadapt ran, I noticed that they use gzip instead of the desired multithreaded pigz.
The docker image affected is: docker://zavolab/cutadapt:1.16-slim.
One quick fix to not waste resources is to set --set-threads remove_adapters_cutadapt=1 remove_polya_cutadapt=1 pe_remove_adapters_cutadapt=1 pe_remove_polya_cutadapt=1 in the snakemake call.
Edited by Dominik Burri